There is discrepancy between characteristics and properties of Russian regional economies regarded as ecological and economic systems, on the one hand, and strategic planning and management tools of economic development, on the other hand. The issue arises because of misperception of the environmental factor as a deterrent to economic growth. All the above necessitates the improvement to the system of diagnostics methods of assessment of real regional sustainability levels. The plausible application outcome of methods suggested in this paper is adjustment of public structural economic policy and methodological bases for monitoring the results of economic, social, and environmental development to the need of sustainable economy.